Parametrization

client/src/actions/index.js

@@ -8,6 +8,7 @@ import {
 import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
 import * as selnActions from "./selection";
 import * as annoActions from "./annotation";
+import * as spatialActions from "./spatial";
 import * as viewActions from "./viewStack";
 import * as embActions from "./embedding";
 import * as genesetActions from "./geneset";
@@ -272,4 +273,5 @@ export default {
   genesetDelete: genesetActions.genesetDelete,
   genesetAddGenes: genesetActions.genesetAddGenes,
   genesetDeleteGenes: genesetActions.genesetDeleteGenes,
+  requestSpatialMetadata: spatialActions.requestSpatialMetadata,
 };

client/src/actions/spatial.js

@@ -0,0 +1,35 @@
+import * as globals from "../globals";
+
+export const requestSpatialMetadata = () => async (dispatch) => {
+  dispatch({ type: "request spatial metadata started" });
+  try {
+    const res = await fetch(
+      `${globals.API.prefix}${globals.API.version}spatial/meta`,
+      {
+        method: "GET",
+        headers: new Headers({
+          Accept: "application/json",
+          "Content-Type": "application/json",
+        }),
+        credentials: "include",
+      }
+    );
+
+    if (!res.ok || res.headers.get("Content-Type") !== "application/json") {
+      return null; // TODO need a dispatch //dispatchDiffExpErrors(dispatch, res);
+    }
+
+    const response = await res.json();
+
+    /* then send the success case action through */
+    return dispatch({
+      type: "request spatial metadata success",
+      data: response,
+    });
+  } catch (error) {
+    return dispatch({
+      type: "request spatial metadata error",
+      error,
+    });
+  }
+};

client/src/components/app.js

@@ -23,6 +23,8 @@ class App extends React.Component {
   componentDidMount() {
     const { dispatch } = this.props;
 
+    dispatch(actions.requestSpatialMetadata());
+
     /* listen for url changes, fire one when we start the app up */
     window.addEventListener("popstate", this._onURLChanged);
     this._onURLChanged();

client/src/components/graph/drawSpatialImageRegl.js

@@ -45,35 +45,15 @@ export default function drawSpatialImageRegl(regl) {
 
     attributes: {
       a_texCoord: [0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0],
-      // a_position: [
+      a_position: regl.prop("rectCoords"),
-      //     10, 0,
-      //     10 + regl.prop("img_width"), 0,
-      //     10, 0 + regl.prop("img_height"),
-      //     10, 0 + regl.prop("img_height"),
-      //     10 + regl.prop("img_width"), 0,
-      //     10 + regl.prop("img_width"), 0 + regl.prop("img_height"),
-      //     ],
-      a_position: [
-        0,
-        0,
-        0 + 1921,
-        0,
-        0,
-        0 + 2000,
-        0,
-        0 + 2000,
-        0 + 1921,
-        0,
-        0 + 1921,
-        0 + 2000,
-      ],
     },
 
     uniforms: {
       projView: regl.prop("projView"),
       u_image: regl.prop("spatialImageAsTexture"),
       color: [1, 0, 0, 1],
-      u_resolution: [1921, 2000],
+      u_resolution: [regl.prop("imageWidth"), regl.prop("imageHeight")],
+      image_width: regl.prop("imageWidth"),
       //   translate:
     },
 

client/src/components/graph/graph.js

@@ -78,6 +78,7 @@ function createModelTF() {
   colors: state.colors,
   pointDilation: state.pointDilation,
   genesets: state.genesets.genesets,
+  spatial: state.spatial.metadata,
 }))
 class Graph extends React.Component {
   static createReglState(canvas) {
@@ -110,19 +111,20 @@ class Graph extends React.Component {
     return !shallowEqual(props.watchProps, prevProps.watchProps);
   }
 
-  computePointPositions = memoize((X, Y, modelTF) => {
+  computePointPositions = memoize((X, Y, modelTF, spatialMetadata) => {
     /*
     compute the model coordinate for each point
     */
     console.log({ X }, { Y });
     const positions = new Float32Array(2 * X.length);
     for (let i = 0, len = X.length; i < len; i += 1) {
-      const p = vec2.fromValues(X[i], Y[i]);
+      // TODO: Introduce the feature flag here
+      // const p = vec2.fromValues(X[i], Y[i]);
+      const p = this.rescalePointForSpatial(X[i], Y[i], spatialMetadata);
       vec2.transformMat3(p, p, modelTF);
       positions[2 * i] = p[0];
       positions[2 * i + 1] = p[1];
     }
-    console.log({ transformed: positions });
     return positions;
   });
 
@@ -238,6 +240,7 @@ class Graph extends React.Component {
       colorBuffer: null,
       flagBuffer: null,
       drawSpatialImage: null,
+      spatial: null,
 
       // component rendering derived state - these must stay synchronized
       // with the reducer state they were generated from.
@@ -452,6 +455,33 @@ class Graph extends React.Component {
     });
   }
 
+  rescalePointForSpatial = (x, y, spatialMetadata) => {
+    // console.log({spatialMetadata});
+    const translate = vec2.fromValues(
+      spatialMetadata.inverseTranslate[0],
+      spatialMetadata.inverseTranslate[1]
+    );
+    const min = vec2.fromValues(
+      spatialMetadata.inverseMin[0],
+      spatialMetadata.inverseMin[1]
+    );
+    const scalefactor = spatialMetadata.scaleref;
+    const wh = vec2.fromValues(
+      spatialMetadata.imageWidth,
+      spatialMetadata.imageHeight
+    );
+
+    // Apply the inverse transform
+    const p = vec2.fromValues(x, y);
+    vec2.sub(p, p, translate);
+    vec2.scale(p, p, spatialMetadata.inverseScale);
+    vec2.add(p, p, min);
+
+    vec2.scale(p, p, scalefactor);
+    vec2.div(p, p, wh);
+    return p;
+  };
+
   setReglCanvas = (canvas) => {
     this.reglCanvas = canvas;
     this.setState({
@@ -534,9 +564,12 @@ class Graph extends React.Component {
       crossfilter,
       pointDilation,
       viewport,
+      spatial,
     } = props.watchProps;
     const { modelTF } = this.state;
 
+    console.log({ spatial });
+
     const [layoutDf, colorDf, pointDilationDf] = await this.fetchData(
       annoMatrix,
       layoutChoice,
@@ -547,7 +580,7 @@ class Graph extends React.Component {
     const { currentDimNames } = layoutChoice;
     const X = layoutDf.col(currentDimNames[0]).asArray();
     const Y = layoutDf.col(currentDimNames[1]).asArray();
-    const positions = this.computePointPositions(X, Y, modelTF);
+    const positions = this.computePointPositions(X, Y, modelTF, spatial.data);
 
     const colorTable = this.updateColorTable(colorsProp, colorDf);
     const colors = this.computePointColors(colorTable.rgb);
@@ -579,6 +612,7 @@ class Graph extends React.Component {
       flags,
       width,
       height,
+      spatial,
     };
   };
 
@@ -760,7 +794,6 @@ class Graph extends React.Component {
     const { positions, colors, flags, height, width } = asyncProps;
     this.cachedAsyncProps = asyncProps;
     const { pointBuffer, colorBuffer, flagBuffer } = this.state;
-    console.log({ pos2: positions });
     let needToRenderCanvas = false;
 
     if (height !== prevAsyncProps?.height || width !== prevAsyncProps?.width) {
@@ -824,20 +857,21 @@ class Graph extends React.Component {
     projectionTF,
     drawSpatialImage
   ) {
-    const { annoMatrix } = this.props;
+    const { annoMatrix, spatial } = this.props;
     if (!this.reglCanvas || !annoMatrix) return;
 
     const { schema } = annoMatrix;
     const cameraTF = camera.view();
     const projView = mat3.multiply(mat3.create(), projectionTF, cameraTF);
     const { width, height } = this.reglCanvas;
+    const imW = spatial.data.imageWidth;
+    const imH = spatial.data.imageHeight;
+
     regl.poll();
     regl.clear({
       depth: 1,
       color: [0, 0, 0, 0],
     });
-    console.log({ pointBuffer });
-    console.log({ projView });
     drawPoints({
       distance: camera.distance(),
       color: colorBuffer,
@@ -850,8 +884,9 @@ class Graph extends React.Component {
     });
     drawSpatialImage({
       projView,
-      img_width: this.spatialImage.width,
+      imageWidth: imW,
-      img_height: this.spatialImage.height,
+      imageHeight: imH,
+      rectCoords: [0, 0, imW, 0, 0, imH, 0, imH, imW, 0, imW, imH],
       spatialImageAsTexture: regl.texture({
         data: this.spatialImage,
         wrapS: "clamp",
@@ -869,10 +904,14 @@ class Graph extends React.Component {
       layoutChoice,
       pointDilation,
       crossfilter,
+      spatial,
     } = this.props;
     const { modelTF, projectionTF, camera, viewport, regl } = this.state;
     const cameraTF = camera?.view()?.slice();
 
+    console.log("---RENDER");
+    console.log({ props: this.props });
+
     return (
       <div
         id="graph-wrapper"
@@ -939,6 +978,7 @@ class Graph extends React.Component {
             pointDilation,
             crossfilter,
             viewport,
+            spatial,
           }}
         >
           <Async.Pending initial>

client/src/reducers/index.js

@@ -11,6 +11,7 @@ import continuousSelection from "./continuousSelection";
 import graphSelection from "./graphSelection";
 import colors from "./colors";
 import differential from "./differential";
+import spatial from "./spatial";
 import layoutChoice from "./layoutChoice";
 import controls from "./controls";
 import annotations from "./annotations";
@@ -38,6 +39,7 @@ const Reducer = undoable(
     ["colors", colors],
     ["controls", controls],
     ["differential", differential],
+    ["spatial", spatial],
     ["centroidLabels", centroidLabels],
     ["pointDilation", pointDialation],
     ["autosave", autosave],
@@ -51,6 +53,7 @@ const Reducer = undoable(
     "colors",
     "controls",
     "differential",
+    "spatial",
     "layoutChoice",
     "centroidLabels",
     "genesets",

client/src/reducers/spatial.js

@@ -0,0 +1,34 @@
+const Spatial = (
+  state = {
+    loading: null,
+    error: null,
+    metadata: null,
+  },
+  action
+) => {
+  switch (action.type) {
+    case "request spatial metadata started":
+      return {
+        ...state,
+        loading: true,
+        error: null,
+      };
+    case "request spatial metadata success":
+      return {
+        ...state,
+        error: null,
+        loading: false,
+        metadata: action,
+      };
+    case "request spatial metadata error":
+      return {
+        ...state,
+        loading: false,
+        error: action.data,
+      };
+    default:
+      return state;
+  }
+};
+
+export default Spatial;

server/app/app.py

@@ -195,6 +195,11 @@ class SpatialImageAPI(Resource):
     def get(self, data_adaptor):
         return common_rest.spatial_image_get(request, data_adaptor)
 
+class SpatialMetaAPI(Resource):
+    @rest_get_data_adaptor
+    def get(self, data_adaptor):
+        return data_adaptor.get_spatial_metadata()
+
 
 def get_api_base_resources(bp_base):
     """Add resources that are accessed from the api url"""
@@ -229,6 +234,7 @@ def get_api_dataroot_resources(bp_dataroot):
     add_resource(LayoutObsAPI, "/layout/obs")
     # Spatial routes
     add_resource(SpatialImageAPI, "/spatial/image")
+    add_resource(SpatialMetaAPI, "/spatial/meta")
     return api
 
 

server/data_anndata/anndata_adaptor.py

@@ -277,6 +277,40 @@ class AnndataAdaptor(DataAdaptor):
     def get_spatial(self):
         return self.data.uns["spatial"]
 
+    def get_spatial_metadata(self):
+        spatial = self.get_spatial()
+
+        resolution = "hires"
+
+        if len(list(spatial)) == 0:
+            raise Exception("uns does not have spatial information")
+
+        library_id = list(spatial)[0]
+
+        if "images" not in spatial[library_id]:
+            raise Exception("spatial information does not contain images")
+
+        if resolution not in spatial[library_id]["images"]:
+            raise Exception(f"spatial information does not contain requested resolution '{resolution}'")
+
+        scaleref = spatial[library_id]["scalefactors"][f"tissue_{resolution}_scalef"]
+        (h, w, _) = spatial[library_id]["images"][resolution].shape
+
+        A = self.data.obsm["X_spatial"]
+        min = np.nanmin(A, axis=0)
+        max = np.nanmax(A, axis=0)
+        scale = np.amax(max - min)
+        translate = 0.5 - ((max - min) / scale / 2)
+
+        return {
+            "imageWidth": w,
+            "imageHeight": h,
+            "scaleref": scaleref,
+            "inverseScale": int(scale),
+            "inverseTranslate": translate.tolist(),
+            "inverseMin": min.tolist(),
+        }
+
     def get_embedding_names(self):
         """
         Return pre-computed embeddings.

server/data_common/data_adaptor.py

@@ -363,10 +363,15 @@ class DataAdaptor(metaclass=ABCMeta):
 
         print(f"scale {scale}, translate {translate}")
 
-        A = embedding * 0.17011142
+        # if True: # if visium
-        A = np.column_stack([A[:, 0] / 1921, A[:, 1] / 2000])
+        #     self.data.uns["spatial"]
 
-        normalized_layout = A.astype(dtype=np.float32)
+
+        # adata.uns["spatial"]['V1_Adult_Mouse_Brain']["scalefactors"]["tissue_hires_scalef"]
+        # A = embedding * 0.17011142
+        # A = np.column_stack([A[:, 0] / 1921, A[:, 1] / 2000])
+
+        # normalized_layout = A.astype(dtype=np.float32)
         return normalized_layout
 
     def layout_to_fbs_matrix(self, fields):